Cadmium in PDB 9r00: De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension.

The structure of De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension., PDB code: 9r00 was solved by M.Nadal, E.Marcos, A.Castellvi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.10 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	40.397, 61.043, 96.117, 90, 90, 90
R / Rfree (%)	21.6 / 26.4

The structure of De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension. also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Cadmium atom in the De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension. (pdb code 9r00). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension., PDB code: 9r00:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in the De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:37.4 occ:0.90 OE2 A:GLU16 1.7 39.9 1.0 CD A:GLU16 2.4 36.6 1.0 OE1 A:GLU16 2.5 39.5 1.0 OE2 A:GLU13 2.6 42.3 1.0 OE1 A:GLU13 2.6 39.2 1.0 CD A:GLU13 2.9 38.9 1.0 NZ A:LYS17 3.8 67.8 1.0 CG A:GLU16 3.9 43.8 1.0 NH2 A:ARG9 4.2 39.3 1.0 CB A:LEU61 4.4 33.6 1.0 CG A:GLU13 4.4 39.4 1.0 NE A:ARG9 4.6 44.7 1.0 CD2 A:LEU61 4.7 34.6 1.0 CB A:GLU16 4.7 47.4 1.0 CZ A:ARG9 4.9 40.6 1.0

Cadmium binding site 2 out of 7 in the De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:33.3 occ:0.36 O A:HOH304 2.1 25.0 1.0 OD2 A:ASP19 2.4 42.0 1.0 OD1 A:ASP19 2.7 40.4 1.0 CG A:ASP19 2.9 42.7 1.0 CB A:GLU21 4.1 63.6 1.0 CB A:ASP19 4.4 41.8 1.0 N A:LEU22 4.4 49.7 1.0 CG A:GLU21 4.6 66.5 1.0 CB A:LEU22 4.7 48.2 1.0 C A:GLU21 5.0 51.0 1.0

Cadmium binding site 3 out of 7 in the De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:70.0 occ:0.63 OE1 A:GLU126 2.5 46.1 1.0 OE2 A:GLU126 2.8 44.7 1.0 CD A:GLU126 3.0 44.4 1.0 OE1 A:GLN130 4.1 51.4 1.0 CE A:LYS133 4.4 60.7 1.0 CG A:GLU126 4.5 42.5 1.0 CG A:GLU129 4.6 47.6 1.0 CB A:GLU129 4.6 32.3 1.0

Cadmium binding site 4 out of 7 in the De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:41.6 occ:0.43 O A:HOH301 1.3 24.9 1.0 OE1 A:GLU129 2.4 58.0 1.0 OE1 A:GLU132 2.4 48.5 1.0 OE2 A:GLU132 3.0 63.5 1.0 CD A:GLU132 3.0 55.0 1.0 CD A:GLU129 3.3 56.1 1.0 OE2 A:GLU129 3.6 67.6 1.0 CG A:GLU132 4.5 51.4 1.0 CG A:GLU129 4.6 47.6 1.0 CB A:GLU132 4.9 48.6 1.0 CA A:GLU129 5.0 32.8 1.0

Cadmium binding site 5 out of 7 in the De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:36.6 occ:0.50 OE1 A:GLU116 2.4 45.3 1.0 OE2 A:GLU116 2.7 55.2 1.0 CD A:GLU116 2.9 47.2 1.0 CL A:CL210 3.6 34.4 0.5 CL A:CL208 3.9 23.0 0.5 CG A:GLU116 4.4 41.9 1.0 ND1 A:HIS113 4.6 34.9 1.0

Cadmium binding site 6 out of 7 in the De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:37.9 occ:0.50 OE2 A:GLU44 1.7 52.7 1.0 CL A:CL209 2.0 25.3 0.5 CD A:GLU44 2.3 45.9 1.0 OE1 A:GLU44 2.4 39.7 1.0 CG A:GLU44 3.8 47.6 1.0 N A:THR41 4.4 39.3 1.0 CB A:THR41 4.7 45.6 1.0 CB A:GLU44 4.7 46.4 1.0 O A:THR39 4.8 47.2 1.0 OG1 A:THR41 4.8 42.2 1.0 O A:THR41 5.0 46.0 1.0 CA A:PHE40 5.0 40.8 1.0

Cadmium binding site 7 out of 7 in the De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of De Novo NTF2-Like Protein with A 2-Helix C-Terminal Extension. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:93.7 occ:0.25 OE2 A:GLU21 3.0 70.7 1.0 CD A:GLU21 3.4 74.2 1.0 OE1 A:GLU21 3.7 73.6 1.0 CG A:GLU21 4.4 66.5 1.0

M.Nadal, J.Albi-Puig, A.Castellvi, P.M.Garcia-Franco, S.Vega, A.Velazquez-Campoy, E.Marcos. Buttressing Ligand-Binding Pockets in De Novo Designed NTF2-Like Domains. Protein Sci. V. 34 70323 2025.
ISSN: ESSN 1469-896X
PubMed: 41074781
DOI: 10.1002/PRO.70323